LAMMPS (4 May 2017)
  using 1 OpenMP thread(s) per MPI task

units           metal

atom_style      atomic
atom_modify     map array
boundary        p p p
atom_modify	sort 0 0.0

# temperature

variable t equal 1800.0

# coordination number cutoff

variable r equal 2.835

# minimization parameters

variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1

# diamond unit cell

variable a equal 5.431
lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431

region          myreg block     0 4                                 0 4                                 0 4
create_box      1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
  1 by 2 by 2 MPI processor grid
create_atoms    1 region myreg
Created 512 atoms

mass            1       28.06

group Si type 1
512 atoms in group Si

velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian

# make a vacancy

group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511

pair_style      edip
pair_coeff * * Si.edip Si
Reading potential file Si.edip with DATE: 2011-09-15

thermo          10

fix             1 all nvt temp $t $t 0.1
fix             1 all nvt temp 1800 $t 0.1
fix             1 all nvt temp 1800 1800 0.1

timestep        1.0e-3
neighbor        1.0 bin
neigh_modify    every 1 delay 10 check yes

# equilibrate

run             500
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.12138
  ghost atom cutoff = 4.12138
  binsize = 2.06069, bins = 11 11 11
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair edip, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1802.3816   -2372.6618            0   -2253.8439    12260.967 
      10    938.75954   -2315.5185            0   -2253.6329    558.21736 
      20    534.27232   -2288.4721            0   -2253.2514    -2710.767 
      30    1043.7796   -2320.9485            0   -2252.1398    8679.4385 
      40    658.09162   -2293.8597            0   -2250.4765    2165.3752 
      50    517.93008   -2283.7238            0   -2249.5805   -1124.9362 
      60    1063.3594   -2318.4409            0   -2248.3414     7277.853 
      70    868.14007   -2304.0133            0   -2246.7832    2050.2859 
      80    826.37803   -2300.0187            0   -2245.5416    91.100098 
      90    1289.6772   -2328.7151            0   -2243.6961    8180.7427 
     100    976.36211   -2305.9371            0   -2241.5727    3614.0511 
     110    810.81711   -2293.4705            0   -2240.0193    1359.3687 
     120     1165.707   -2314.9026            0    -2238.056    7336.4505 
     130    929.81248    -2297.139            0   -2235.8432    2793.8463 
     140    804.47872   -2287.2074            0    -2234.174    704.92524 
     150     1182.414   -2310.0266            0   -2232.0787    7822.2339 
     160    979.92395   -2294.2969            0   -2229.6977    3206.7474 
     170    830.14746   -2282.6079            0   -2227.8824   -296.87288 
     180    1271.1133   -2309.4274            0   -2225.6322     7199.614 
     190    1209.6006   -2302.6407            0   -2222.9006    5528.3799 
     200    954.67692   -2283.6621            0   -2220.7272     47.02925 
     210     1260.814   -2301.5582            0    -2218.442    4829.7879 
     220    1274.9954   -2299.7285            0   -2215.6774    5518.0611 
     230    1048.0074    -2282.398            0   -2213.3106    1754.4157 
     240    1261.7071   -2294.1107            0   -2210.9356    5233.2714 
     250    1272.6179   -2292.0793            0   -2208.1849     4795.934 
     260    989.14207   -2271.0278            0   -2205.8209   -820.18098 
     270    1212.0444   -2283.4212            0     -2203.52    3395.8631 
     280    1391.9572   -2292.3809            0   -2200.6194    6666.2464 
     290    1093.1205   -2270.0421            0   -2197.9807    206.94752 
     300     1159.483    -2272.102            0   -2195.6657    778.53823 
     310    1407.3528   -2285.6227            0   -2192.8463    5223.0487 
     320    1236.7164   -2271.5389            0   -2190.0112    1865.3963 
     330    1258.8275   -2270.4611            0   -2187.4758     2333.321 
     340    1507.9519   -2283.9906            0   -2184.5824     6775.546 
     350    1366.5116   -2271.7287            0   -2181.6446    3432.1175 
     360    1305.2828   -2265.1091            0   -2179.0614    1498.4079 
     370    1581.4334   -2280.4645            0   -2176.2122    6518.5598 
     380    1589.5319   -2277.9428            0   -2173.1566    6334.6527 
     390    1402.6782   -2262.9323            0    -2170.464    3278.3048 
     400    1374.9587   -2258.5717            0   -2167.9307    3608.7293 
     410    1295.7416   -2250.7752            0   -2165.3565    1877.5245 
     420    1278.6727   -2247.1099            0   -2162.8164    1599.4189 
     430    1508.1328   -2259.4245            0   -2160.0044    4300.2235 
     440    1624.2957   -2263.9806            0   -2156.9026    4432.6267 
     450    1597.3356    -2259.263            0   -2153.9623    3370.3829 
     460    1772.0921   -2267.9105            0   -2151.0895    5788.3219 
     470    1806.4047    -2267.304            0    -2148.221    5950.1188 
     480    1593.0406   -2250.7469            0   -2145.7294    2518.0601 
     490    1660.9766    -2252.894            0    -2143.398    4282.1654 
     500    1714.2831   -2253.9295            0   -2140.9194    5740.0268 
Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms

Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.074678   | 0.077817   | 0.084705   |   1.4 | 71.01
Neigh   | 0.0036662  | 0.0037943  | 0.0039661  |   0.2 |  3.46
Comm    | 0.013665   | 0.020312   | 0.023178   |   2.7 | 18.54
Output  | 0.0010247  | 0.0010931  | 0.0012922  |   0.3 |  1.00
Modify  | 0.0043213  | 0.0047521  | 0.0051889  |   0.6 |  4.34
Other   |            | 0.001814   |            |       |  1.66

Nlocal:    127.75 ave 131 max 124 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:    433.75 ave 441 max 426 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  1979.5 ave 2040 max 1895 min
Histogram: 1 0 0 0 1 0 0 0 0 2

Total # of neighbors = 7918
Ave neighs/atom = 15.4951
Neighbor list builds = 19
Dangerous builds = 0

Total wall time: 0:00:00
